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Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

机译:单细胞转录组学揭示免疫细胞中表达和剪接的双峰性

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摘要

Recent molecular studies have shown that, even when derived from a seemingly homogenous population, individual cells can exhibit substantial differences in gene expression, protein levels and phenotypic output, with important functional consequences. Existing studies of cellular heterogeneity, however, have typically measured only a few pre-selected RNAs or proteins simultaneously, because genomic profiling methods could not be applied to single cells until very recently. Here we use single-cell RNA sequencing to investigate heterogeneity in the response of mouse bone-marrow-derived dendritic cells (BMDCs) to lipopolysacchar-ide. We find extensive, and previously unobserved, bimodal variation in messenger RNA abundance and splicing patterns, which we validate by RNA-fluorescence in situ hybridization for select transcripts. In particular, hundreds of key immune genes are bimodally expressed across cells, surprisingly even for genes that are very highly expressed at the population average. Moreover, splicing patterns demonstrate previously unobserved levels of heterogeneity between cells. Some of the observed bimodality can be attributed to closely related, yet distinct, known maturity states of BMDCs; other portions reflect differences in the usage of key regulatory circuits. For example, we identify a module of 137 highly variable, yet co-regulated, antiviral response genes. Using cells from knockout mice, we show that variability in this module may be propagated through an interferon feedback circuit, involving the transcriptional regulators Stat2 and Irf7. Our study demonstrates the power and promise of single-cell genomics in uncovering functional diversity between cells and in deciphering cell states and circuits.
机译:最近的分子研究表明,即使是从看似均一的种群中衍生出来的,单个细胞也可能在基因表达,蛋白质水平和表型输出方面表现出实质性差异,并具有重要的功能后果。但是,有关细胞异质性的现有研究通常只能同时测量几种预选的RNA或蛋白质,因为直到最近才将基因组谱分析方法应用于单个细胞。在这里,我们使用单细胞RNA测序来研究小鼠骨髓来源的树突状细胞(BMDC)对脂多糖的反应中的异质性。我们在信使RNA丰度和剪接模式中发现了广泛的,以前没有观察到的双峰变化,我们通过RNA荧光原位杂交对选定的转录本进行了验证。特别是,数百种关键免疫基因在细胞中双峰表达,甚至对于在群体平均水平上非常高表达的基因也令人惊讶。此外,剪接模式表明以前无法观察到的细胞之间的异质性水平。一些观察到的双峰态可以归因于BMDC的紧密相关但又不同的已知成熟状态。其他部分则反映了关键监管电路在用法上的差异。例如,我们确定了137个高度可变但又共同调节的抗病毒应答基因的模块。使用来自敲除小鼠的细胞,我们显示该模块中的变异性可能通过干扰素反馈电路传播,涉及转录调节子Stat2和Irf7。我们的研究证明了单细胞基因组学在揭示细胞之间功能多样性以及破译细胞状态和电路方面的力量和希望。

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  • 来源
    《Nature》 |2013年第7453期|236-240|共5页
  • 作者单位

    Department of Chemistry and Chemical Biology and Department of Physics, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA;

    Broad Institute of MIT and Harvard. 7 Cambridge Center, Cambridge, Massachuestts 02142, USA;

    Broad Institute of MIT and Harvard. 7 Cambridge Center, Cambridge, Massachuestts 02142, USA;

    Department of Chemistry and Chemical Biology and Department of Physics, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA;

    Department of Chemistry and Chemical Biology and Department of Physics, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA;

    Broad Institute of MIT and Harvard. 7 Cambridge Center, Cambridge, Massachuestts 02142, USA;

    Broad Institute of MIT and Harvard. 7 Cambridge Center, Cambridge, Massachuestts 02142, USA;

    Broad Institute of MIT and Harvard. 7 Cambridge Center, Cambridge, Massachuestts 02142, USA;

    Broad Institute of MIT and Harvard. 7 Cambridge Center, Cambridge, Massachuestts 02142, USA;

    Broad Institute of MIT and Harvard. 7 Cambridge Center, Cambridge, Massachuestts 02142, USA;

    Broad Institute of MIT and Harvard. 7 Cambridge Center, Cambridge, Massachuestts 02142, USA;

    Broad Institute of MIT and Harvard. 7 Cambridge Center, Cambridge, Massachuestts 02142, USA;

    Broad Institute of MIT and Harvard. 7 Cambridge Center, Cambridge, Massachuestts 02142, USA;

    Broad Institute of MIT and Harvard. 7 Cambridge Center, Cambridge, Massachuestts 02142, USA,Department of Pathology & Center for Systems Biology and Center for Cancer Research, Massachusetts General Hospital, Charlestown,Massachusetts 02129, USA;

    Broad Institute of MIT and Harvard. 7 Cambridge Center, Cambridge, Massachuestts 02142, USA,Center for Immunology and Inflammatory Diseases & Department of Medicine, Massachusetts General Hospital, Charlestown, Massachuestts 02129, USA;

    Broad Institute of MIT and Harvard. 7 Cambridge Center, Cambridge, Massachuestts 02142, USA;

    Department of Chemistry and Chemical Biology and Department of Physics, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA,Broad Institute of MIT and Harvard. 7 Cambridge Center, Cambridge, Massachuestts 02142, USA;

    Broad Institute of MIT and Harvard. 7 Cambridge Center, Cambridge, Massachuestts 02142, USA,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02140, USA;

  • 收录信息 美国《科学引文索引》(SCI);美国《工程索引》(EI);美国《生物学医学文摘》(MEDLINE);美国《化学文摘》(CA);
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